In order to provide rational and feasible schemes to protect the safety of the existed viaduct, the applicable effects of the ground grouting pre-reinforcement scheme and the antifriction schemes using the thixotropic muds with different grouting volumes which are adopted in the rectangular pipe jacking construction of the underpass of Juhua Metro Station on Kunming Rail Transit Line No. 4 in soft soils on protecting the existed adjacent viaduct are studied by numerical simulation. The analytical results show that: (1) The grouting pre-reinforcement of soils between viaduct piles and the jacking pipe can significantly reduce the transverse deformation of viaduct piles during the pipe jacking construction, and the reduction magnitude can reach 34%. (2) The influence of the pipe-soil friction on viaduct piles can be effectively reduced by using the over-grouting scheme of the thixotropic mud in the construction process, and the maximum longitudinal deformation of viaduct piles can be reduced by 28% compared with that when the normal-grouting scheme of the thixotropic mud is adopted. (3) The simultaneous adoption of the pre-reinforcement of soils between viaduct piles and the jacking pipe and the over-grouting scheme of the thixotropic mud can ensure the safety of the viaduct structure during the construction of the jacking pipe.